title: Dnmt3a_WT_PROseq_rep3

description:
Nascent RNA
3WT_3Dnmt3a_cKO_proseq_mapped_to_all_genes_over_3000_TSS.txt
3WT_3Dnmt3a_cKO_proseq_mapped_to_all_genes_over_3000_gene_body.txt

data_processing:
Random hexanucleotide barcodes included in sequencing adaptors permitted the identification and removal of PCR duplicates using Clumpify (BBTools v37.90).
Reads were trimmed to 25 bp and mapped to the mm10 reference genome using Bowtie2 (v2.2.9).
Reads were converted to BED format using BEDTools (v2.26.0) and trimmed to the width of a single nucleotide at the second-to-3’ position, corresponding to the position of RNA Polymerase II before the incorporation of the terminal 11-biotin-NTP.
PRO-seq reads were quantified in Refseq transcription start sites (TSS: -1kb to +1kb) and gene bodies (TSS +1kb to TTS) using BEDOPS (v2.4.30).
Genome_build: mm10
Supplementary_files_format_and_content: Table of raw PRO-seq read counts in TSS (-1kb to +1kb) or gene body (TSS +1kb to TTS) for all genes greater than 3000 bp in length.

extract_protocol:
Forebrain (cortex and hippocampus) was dissected from 8-to-12-week-old MeCP2 KO, MeCP2 R306C, Dnmt3a cKO mice and their respective WT littermate controls. Tissue was homogenized in ice-cold PBS using a Dounce homogenizer, and nuclei were pelleted by spinning at 17,000 g for 5 minutes at 4°C. Chromatin isolation was performed as previously described (Chu et al., 2018). Nuclei were resuspended in lysis buffer (NUN: 0.3 M NaCl, 1 M Urea, 20 mM HEPES pH 7.5, 7.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40, 1 mM DTT, cOmplete Protease Inhibitor (Roche), 40 units/mL SUPERase In RNase Inhibitor (Invitrogen)) and incubated on ice for 30 minutes. Lysed nuclei were centrifuged at 12,500 g for 30 minutes at 4°C. The resulting insoluble chromatin pellet was washed in 50 mM Tris-HCl pH 7.5 and placed in 50 μL chromatin storage buffer (25% glycerol, 50 mM Tris-HCl pH 8.0, 5 mM MgAc2, 0.1 mM EDTA, 5 mM DTT, 40 units/mL SUPERase In RNase Inhibitor). Chromatin was solubilized by sonicating on a Diagenode Bioruptor (High Power, 40 cycles, 30 seconds on/30 seconds off). Solubilized chromatin was flash-frozen in liquid nitrogen and stored at -80 °C. PRO-seq RNA purification was performed as previously described (Kwak et al., 2013; Mahat et al., 2016). Frozen chromatin was thawed on ice and combined with 50 μL 2X Run-on Buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 300 mM KCl, 40 μM Biotin-11-ATP, 40 μM Biotin-11-GTP, 40 μM Biotin-11-CTP, 40 μM Biotin-11-UTP, 1% Sarksosyl, 1 mM DTT, 0.8 units/μL SUPERase In RNase Inhibitor). The reaction was incubated at 37°C for 5 minutes and then quenched with 500 μL Trizol LS, combined with 130 μL chloroform, and centrifuged at 17,000g for 5 minutes at 4 °C. The aqueous layer containing RNA was combined with 1 mL ice-cold ethanol and 2.5 μL GlycoBlue (Invitrogen) and centrifuged at 17,000g for 15 minutes at 4 °C. The RNA pellet was washed in 75% ethanol, air-dried, and resuspended in 20 μL nuclease-free water. RNA was hydrolyzed by adding 5 μL 1 N NaOH and incubating for 4 minutes at 4°C, then neutralized with 30 μL 1 M Tris-HCl pH 7.0. Hydrolyzed RNA was run on a Micro Bio-Spin P-30 Column (Bio-Rad) to remove excess salts. Biotinylated RNA was purified with magnetic streptavidin beads (NEB) at room temperature for 20 minutes and washed 2 times each with 500 μL High-Salt (2 M NaCl, 50 mM Tris-HCl pH 7.4, 0.5% Triton X-100, 4 units/mL SUPERase In RNase Inhibitor), Binding (300 mM NaCl, 10 mM Tris-HCl pH 7.4, 0.1% Triton X-100, 4 units/mL SUPERase In RNase Inhibitor), and Low-Salt (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100, 4 units/mL SUPERase In RNase Inhibitor) wash buffers. Beads were resuspended in 300 μL Trizol, and combined with 60 μL chloroform, and RNA was purified as above.
PRO-seq library preparation was performed as previously described (Kwak et al., 2013; Mahat et al., 2016). The dried RNA pellet was resuspended in 4 μL of 12.5 μM Reverse 3’ RNA adaptor and used to make a T4 RNA Ligase I reaction mix (5 μM Reverse 3’ RNA Adaptor, 1X T4 RNA Ligase I Buffer, 1 mM ATP, 10 units T4 RNA Ligase I, 10% PEG 8000, 2 units/μL SUPERase In RNase Inhibitor). The reaction was incubated overnight at 20°C. The ligated RNA was purified with magnetic streptavidin beads, washed, and extracted with Trizol as above. The RNA was treated with RNA 5' Pyrophosphohydrolase (RppH) to remove the 5’ cap (1X NEBuffer 2, 10 units RppH, 0.2 units/μL SUPERase In RNase Inhibitor) and incubated for 1 hour at 37°C. A hydroxyl repair reaction mix (1X PNK Buffer, 1 mM ATP, 25 units PNK, 0.2 units/μL SUPERase In RNase Inhibitor) was added directly to the Rpph reaction and incubated for an additional hour at 37°C. RNA was extracted with Trizol as above. The dried RNA pellet was resuspended in 4 μL of 12.5 μM Reverse 5’ RNA adaptor and used to make a T4 RNA Ligase I reaction mix (5 μM Reverse 5’ RNA Adaptor, 1X T4 RNA Ligase I Buffer, 1 mM ATP, 10 units T4 RNA Ligase I, 10% PEG 8000, 2 units/μL SUPERase In RNase Inhibitor). The reaction was incubated overnight at 20°C. The ligated RNA was purified with magnetic streptavidin beads, washed, and extracted with Trizol as above. The resulting RNA library was reverse transcribed using SuperScript III Reverse Transcriptase (Invitrogen). The cDNA libraries were amplified using Q5 DNA Polymerase (NEB) for 14 cycles or more, as determined by a test amplification with diluted cDNA. Amplified libraries were purified on Agencourt RNAClean XP beads.
PRO-seq

value: 8-12 weeks

value: Dnmt3a fl/fl


title: Dnmt3a_KO_PROseq_rep1

status: Public on Nov 26 2019

type: SRA

city: Boston

first: Lisa

middle: D.

last: Boxer

state: MA

address: 220 Longwood Ave., Goldenson Bldg Rm 405

department: Neurobiology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Forebrain tissue

tag: strain

tag: age

tag: gender

value: Female

tag: genotype

value: Nestin-cre; Dnmt3a fl/fl


title: Dnmt3a_KO_PROseq_rep2

value: Male


title: Dnmt3a_WT_PROseq_rep2


title: Dnmt3a_KO_PROseq_rep3


title: R306C_PROseq_rep5

description:
Nascent RNA
5WT_5R306C_proseq_mapped_to_all_genes_over_3000_TSS.txt
5WT_5R306C_proseq_mapped_to_all_genes_over_3000_gene_body.txt

value: MeCP2 R306C


title: Dnmt3a_WT_PROseq_rep1


title: MeCP2_WT_0min_FP_PROseq_rep1

description:
Nascent RNA
FP_PROseq_WT_MeCP2_KO_0_20_40_60_min_mapped_to_all_genes_TSS.txt

data_processing:
Random hexanucleotide barcodes included in sequencing adaptors permitted the identification and removal of PCR duplicates using Clumpify (BBTools v37.90).
Reads were trimmed to 25 bp and mapped to the mm10 reference genome using Bowtie2 (v2.2.9).
Reads were converted to BED format using BEDTools (v2.26.0) and trimmed to the width of a single nucleotide at the second-to-3’ position, corresponding to the position of RNA Polymerase II before the incorporation of the terminal 11-biotin-NTP.
To quantify initiated Pol II signal, PRO-seq reads were counted in -500 to +500 bp of the TSS using bedtools map. Initiation rates were calculated as the linear fit of 0 minute, 20 minute, and 40 minute initiated Pol II PRO-seq signal over time using the lm function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Table of raw PRO-seq read counts in TSS (-500bp to +500bp) for all genes.

extract_protocol:
One side of each forebrain was used for PRO-seq. Cells were permeabilized as described previously (Mahat et al., 2016), with minor modifications. Tissue was dounce homogenized in 5 mL cold PBS, then spun at 800g for 4 minutes at 4°C. The pellet was washed with 10 mL PBS, then spun at 800g for 4 minutes at 4°C. The pellet was resuspended in 1 mL Buffer W (10 mM Tris pH 8, 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 0.5 mM DTT, 10% glycerol) and then 9 mL Buffer P was added (Buffer W with 0.1% Igepal). Lysate was filtered through a 40μm cell strainer and spun at 800g for 4 minutes at 4°C. The pellet was resuspended in 1 mL Buffer W and then 9 mL Buffer P was added. Lysate was incubated on ice for 1 minute, then spun at 800g for 4 minutes at 4°C. The pellet was resuspended in 500 μL Buffer F (50 mM Tris pH 8, 40% glycerol, 5 mM MgCl2, 0.5 mM DTT) and spun at 1000g for 4 minutes at 4°C. The pellet was resuspended in 50 μL Buffer F with 0.5 μL RNase inhibitor (SUPERase In, Ambion), flash frozen, and stored at -80°C. PRO-seq RNA purification was performed as previously described (Kwak et al., 2013; Mahat et al., 2016). Frozen chromatin was thawed on ice and combined with 50 μL 2X Run-on Buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 300 mM KCl, 40 μM Biotin-11-ATP, 40 μM Biotin-11-GTP, 40 μM Biotin-11-CTP, 40 μM Biotin-11-UTP, 1% Sarksosyl, 1 mM DTT, 0.8 units/μL SUPERase In RNase Inhibitor). The reaction was incubated at 37°C for 5 minutes and then quenched with 500 μL Trizol LS, combined with 130 μL chloroform, and centrifuged at 17,000g for 5 minutes at 4 °C. The aqueous layer containing RNA was combined with 1 mL ice-cold ethanol and 2.5 μL GlycoBlue (Invitrogen) and centrifuged at 17,000g for 15 minutes at 4 °C. The RNA pellet was washed in 75% ethanol, air-dried, and resuspended in 20 μL nuclease-free water. RNA was hydrolyzed by adding 5 μL 1 N NaOH and incubating for 4 minutes at 4°C, then neutralized with 30 μL 1 M Tris-HCl pH 7.0. Hydrolyzed RNA was run on a Micro Bio-Spin P-30 Column (Bio-Rad) to remove excess salts. Biotinylated RNA was purified with magnetic streptavidin beads (NEB) at room temperature for 20 minutes and washed 2 times each with 500 μL High-Salt (2 M NaCl, 50 mM Tris-HCl pH 7.4, 0.5% Triton X-100, 4 units/mL SUPERase In RNase Inhibitor), Binding (300 mM NaCl, 10 mM Tris-HCl pH 7.4, 0.1% Triton X-100, 4 units/mL SUPERase In RNase Inhibitor), and Low-Salt (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100, 4 units/mL SUPERase In RNase Inhibitor) wash buffers. Beads were resuspended in 300 μL Trizol, and combined with 60 μL chloroform, and RNA was purified as above.
PRO-seq library preparation was performed as previously described (Kwak et al., 2013; Mahat et al., 2016). The dried RNA pellet was resuspended in 4 μL of 12.5 μM Reverse 3’ RNA adaptor and used to make a T4 RNA Ligase I reaction mix (5 μM Reverse 3’ RNA Adaptor, 1X T4 RNA Ligase I Buffer, 1 mM ATP, 10 units T4 RNA Ligase I, 10% PEG 8000, 2 units/μL SUPERase In RNase Inhibitor). The reaction was incubated overnight at 20°C. The ligated RNA was purified with magnetic streptavidin beads, washed, and extracted with Trizol as above. The RNA was treated with RNA 5' Pyrophosphohydrolase (RppH) to remove the 5’ cap (1X NEBuffer 2, 10 units RppH, 0.2 units/μL SUPERase In RNase Inhibitor) and incubated for 1 hour at 37°C. A hydroxyl repair reaction mix (1X PNK Buffer, 1 mM ATP, 25 units PNK, 0.2 units/μL SUPERase In RNase Inhibitor) was added directly to the Rpph reaction and incubated for an additional hour at 37°C. RNA was extracted with Trizol as above. The dried RNA pellet was resuspended in 4 μL of 12.5 μM Reverse 5’ RNA adaptor and used to make a T4 RNA Ligase I reaction mix (5 μM Reverse 5’ RNA Adaptor, 1X T4 RNA Ligase I Buffer, 1 mM ATP, 10 units T4 RNA Ligase I, 10% PEG 8000, 2 units/μL SUPERase In RNase Inhibitor). The reaction was incubated overnight at 20°C. The ligated RNA was purified with magnetic streptavidin beads, washed, and extracted with Trizol as above. The resulting RNA library was reverse transcribed using SuperScript III Reverse Transcriptase (Invitrogen). The cDNA libraries were amplified using Q5 DNA Polymerase (NEB) for 14 cycles or more, as determined by a test amplification with diluted cDNA. Amplified libraries were purified on Agencourt RNAClean XP beads.
PRO-seq

treatment_protocol: Flavopiridol hydrochloride (Tocris Bioscience) was prepared at 4 mg/mL in a 10% DMSO solution in PBS and injected intraperitoneally at a dose of 50 mg/kg into 8-week-old male WT or MeCP2 KO mice. 20, 40, or 60 minutes after flavopiridol injection, forebrain tissue was dissected and flash frozen. For the “0 minute” timepoint, mice were injected with a control solution of 10% DMSO in PBS and dissected after 40 minutes.

value: 8 weeks

value: WT

tag: fp treatment

value: 0 minutes


title: R306C_PROseq_rep4


title: MeCP2_WT_40min_FP_PROseq_rep3

value: 40 minutes


title: MeCP2_WT_60min_FP_PROseq_rep1

value: 60 minutes


title: R306C_PROseq_rep2


title: R306C_PROseq_rep1


title: WT_PROseq_rep5


title: R306C_PROseq_rep3


title: MeCP2_WT_20min_FP_PROseq_rep1

value: 20 minutes


title: MeCP2_WT_60min_FP_PROseq_rep2


title: MeCP2_KO_0min_FP_PROseq_rep2

value: MeCP2 KO


title: WT_PROseq_rep1


title: WT_PROseq_rep3


title: WT_PROseq_rep2


title: MeCP2_KO_PROseq_rep5

description:
Nascent RNA
5WT_5MeCP2KO_proseq_mapped_to_all_genes_over_3000_TSS.txt
5WT_5MeCP2KO_proseq_mapped_to_all_genes_over_3000_gene_body.txt


title: MeCP2_KO_PROseq_rep3


title: MeCP2_KO_PROseq_rep1


title: MeCP2_KO_PROseq_rep4


title: WT_PROseq_rep4


title: MeCP2_WT_PROseq_rep5


title: MeCP2_KO_PROseq_rep2


title: MeCP2_WT_PROseq_rep2


title: MeCP2_WT_PROseq_rep4


title: WT_cortical_neurons_6hKCl_YY1_input

description: DIV7_0h6hKCl_YY1_motifs_in_YY1_peaks.txt

library_source: genomic

data_processing:
Sequencing reads were trimmed with Trimmomatic (v0.36) to remove adaptors and low quality sequence (settings: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50).
Trimmed reads were mapped to the mm10 genome with Bowtie2 (v2.2.9) with default parameters.
PCR duplicate reads were removed with Samtools (v0.1.19) rmdup.
Reads were extended to 250 bp (to approximate fragment length) with UCSC tools bedextendranges.
For each ChIP antibody, reads for each sample were randomly down-sampled to equal numbers using the GNU shuf utility.
ChIP-seq reads were quantified in the genomic regions specified in figure legends using Bedtools map (v2.26).
Genome_build: mm10
Supplementary_files_format_and_content: Tables of raw ChIP read counts in either full gene bodies (transcription start site (TSS) to transcription termination site (TTS) of longest isoform), gene bodies excluding the first 3kb (TSS +3kb to TTS), or TSS (TSS -1kb to +1kb). For YY1 ChIP, file contains position of YY1 motifs in YY1 peaks.

molecule: genomic DNA

source_name: Cortical neurons

extract_protocol:
Forebrain (cortex and hippocampus) was dissected from 8-to-12-week-old male mice and flash frozen. Tissue was homogenized in 1% formaldehyde and cross-linked for 10 minutes at room temperature. Cross-linking was quenched with 125 mM glycine for 5 minutes at room temperature. Tissue was pelleted by spinning at 500 g for 5 minutes at 4°C, washed once with PBS, then spun again at 500 g for 5 minutes at 4°C. Cells were lysed by resuspending in L1 buffer (50 mM Hepes pH 7.5, 140mM NaCl, 1 mM EDTA pH 8, 1 mM EGTA pH 8, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitors) and rotating at 4°C for 10 minutes, then spun at 500 g for 5 minutes at 4°C. Nuclei were washed for 10 minutes at 4°C in L2 buffer (10 mM Tris pH 8, 200 mM NaCl, protease inhibitors), then spun at 500 g for 5 minutes at 4°C. Nuclei were resuspended in LB3 buffer (10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine, protease inhibitors), and sonicated in a Diagenode Bioruptor (High Power, 60 cycles, 30 seconds on/45 seconds off). Insoluble material was removed by spinning at 16,000 g for 10 minutes at 4°C, and Triton X-100 was added to soluble chromatin at a final concentration of 1%. Chromatin was pre-cleared for two hours with Protein A (for rabbit antibodies) or Protein G (for mouse antibodies) Dynabeads, then incubated with Protein A or Protein G Dynabeads conjugated to antibodies overnight at 4°C. Antibodies used were: H3K27ac (Abcam ab4729), H3K36me3 (Abcam ab9050), H4K12ac (Millipore 07-595), H3K9ac (Millipore 06-942), H3K79me2 (Abcam ab3594), Pol II (Abcam ab817), Pol II Ser5p (Millipore 04-1572), and MeCP2 (Chen et al., 2003). Beads were washed twice with Low Salt Buffer (20 mM Tris pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20 mM Tris pH 8, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with LiCl Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 1% NP-40, 250 mM LiCl, 1% sodium deoxycholate) and once with TE Buffer (50 mM Tris pH 8, 10 mM EDTA) at 4°C. Chromatin was eluted off beads by incubating in TE Buffer with 1% SDS at 65°C for one hour, and crosslinks were reversed by incubating overnight at 65°C. Chromatin was treated with RNase A for 30 minutes at 37°C and Proteinase K for 2 hours at 55°C. DNA was phenol-chloroform extracted and purified with the Qiagen PCR purification kit.
Libraries were generated using the NuGEN Ovation Ultralow System V2 following manufacturer instructions.

value: E16.5 with 7DIV culture

value: Male and female

tag: chip antibody


title: WT_H3K79me2_input_rep1

description: WT_H3K79me2_ChIPseq_input_gene_body_counts.txt


title: WT_cortical_neurons_0hKCl_YY1_ChIPseq

value: YY1 (Abcam ab109237)


title: MeCP2_WT_PROseq_rep1


title: MeCP2_WT_PROseq_rep3


title: R306C_PolII_input_rep2

description: 2WT_2R306C_PolII_Ser5p_ChIPseq_input_TSS_counts.txt


title: WT_H3K79me2_ChIPseq_rep2

value: H3K79me2 (Abcam ab3594)


title: WT_cortical_neurons_6hKCl_YY1_ChIPseq


title: R306C_PolII_Ser5p_ChIPseq_rep2

value: 8-12 weeks

value: Pol II Ser5p (Millipore 04-1572)


title: WT_PolII_input_rep2


title: R306C_PolII_Ser5p_ChIPseq_rep1


title: WT_PolII_input_rep1


title: WT_PolII_Ser5p_ChIPseq_rep2


title: WT_PolII_Ser5p_ChIPseq_rep1


title: R306C_PolII_ChIPseq_rep2

value: Pol II (Abcam ab817)


title: WT_PolII_ChIPseq_rep2


title: WT_PolII_ChIPseq_rep1


title: R306C_PolII_ChIPseq_rep1


title: R306C_input_rep5

description:
WT_R306C_H3K9ac_H4K12ac_H3K27ac_ChIPseq_input_TSS_counts.txt
WT_R306C_H3K9ac_H4K12ac_H3K27ac_ChIPseq_input_TSSplus3kb_to_TTS_counts.txt
4WT_4R306C_MeCP2_ChIPseq_input_TSSplus3kb_to_TTS_counts.txt


title: WT_H3K79me2_ChIPseq_rep1


title: WT_input_rep5


title: R306C_input_rep1

description:
WT_R306C_H3K9ac_H4K12ac_H3K27ac_ChIPseq_input_TSS_counts.txt
WT_R306C_H3K9ac_H4K12ac_H3K27ac_ChIPseq_input_TSSplus3kb_to_TTS_counts.txt


title: WT_input_rep2


title: R306C_PolII_input_rep1


title: R306C_input_rep2


title: WT_H3K79me2_input_rep2


title: WT_input_rep1


title: R306C_MeCP2_ChIPseq_rep4

description: 4WT_4R306C_MeCP2_ChIPseq_input_TSSplus3kb_to_TTS_counts.txt

value: MeCP2 (Chen et al., 2003)


title: WT_input_rep4

value: Male


title: WT_input_rep3


title: R306C_MeCP2_ChIPseq_rep3


title: R306C_MeCP2_ChIPseq_rep2


title: R306C_input_rep4


title: R306C_MeCP2_ChIPseq_rep1


title: WT_MeCP2_ChIPseq_rep3


title: WT_MeCP2_ChIPseq_rep2


title: WT_H4K12ac_ChIPseq_rep3

value: H4K12ac (Millipore 07-595)


title: WT_H4K12ac_ChIPseq_rep1


title: WT_MeCP2_ChIPseq_rep1


title: R306C_H4K12ac_ChIPseq_rep1


title: R306C_input_rep3


title: R306C_H3K27ac_ChIPseq_rep2

value: H3K27ac (Abcam ab4729)


title: R306C_H4K12ac_ChIPseq_rep2


title: R306C_H3K27ac_ChIPseq_rep1


title: WT_MeCP2_ChIPseq_rep4

value: WT


title: WT_H4K12ac_ChIPseq_rep2


title: WT_H3K27ac_ChIPseq_rep1


title: R306C_H3K9ac_ChIPseq_rep3

value: H3K9ac (Millipore 06-942)


title: WT_H3K27ac_ChIPseq_rep2


title: R306C_H3K9ac_ChIPseq_rep1


title: MeCP2_KO_PolII_input_rep1

description: 2WT_2MeCP2_KO_PolII_ChIPseq_input_TSS_counts.txt

value: 8 weeks


title: R306C_H4K12ac_ChIPseq_rep3


title: R306C_H3K9ac_ChIPseq_rep5


title: R306C_H3K9ac_ChIPseq_rep2


title: R306C_H3K9ac_ChIPseq_rep4


title: WT_H3K9ac_ChIPseq_rep1


title: WT_H3K9ac_ChIPseq_rep3


title: WT_H3K9ac_ChIPseq_rep2


title: MeCP2_KO_PolII_input_rep2


title: WT_H3K9ac_ChIPseq_rep4


title: WT_H3K9ac_ChIPseq_rep5


title: MeCP2_WT_PolII_input_rep1


title: MeCP2_KO_PolII_ChIPseq_rep2


title: MeCP2_WT_PolII_ChIPseq_rep1


title: MeCP2_WT_PolII_ChIPseq_rep2


title: MeCP2_WT_PolII_input_rep2


title: MeCP2_KO_input_rep6

description:
10WT_10MeCP2_KO_H3K36me3_ChIPseq_input_gene_body_counts.txt
10WT_10MeCP2_KO_H3K27ac_ChIPseq_input_TSS_counts.txt
10WT_10MeCP2_KO_H3K27ac_ChIPseq_input_TSSplus3kb_to_TTS_counts.txt


title: MeCP2_KO_PolII_ChIPseq_rep1


title: MeCP2_KO_input_rep4


title: MeCP2_KO_input_rep3


title: MeCP2_KO_input_rep9


title: MeCP2_KO_input_rep8


title: MeCP2_KO_input_rep1


title: MeCP2_KO_input_rep7


title: MeCP2_WT_input_rep10


title: MeCP2_WT_input_rep7


title: MeCP2_KO_input_rep5


title: MeCP2_KO_input_rep2


title: MeCP2_WT_input_rep8


title: MeCP2_WT_input_rep3


title: MeCP2_WT_input_rep4


title: MeCP2_WT_input_rep9


title: MeCP2_WT_input_rep1


title: MeCP2_WT_input_rep6


title: MeCP2_KO_H3K27ac_ChIPseq_rep7

description:
10WT_10MeCP2_KO_H3K27ac_ChIPseq_input_TSS_counts.txt
10WT_10MeCP2_KO_H3K27ac_ChIPseq_input_TSSplus3kb_to_TTS_counts.txt


title: MeCP2_WT_input_rep2


title: MeCP2_KO_input_rep10


title: MeCP2_KO_H3K27ac_ChIPseq_rep5


title: MeCP2_KO_H3K27ac_ChIPseq_rep8


title: MeCP2_KO_H3K27ac_ChIPseq_rep3


title: MeCP2_KO_H3K27ac_ChIPseq_rep2


title: MeCP2_WT_H3K27ac_ChIPseq_rep9


title: MeCP2_KO_H3K27ac_ChIPseq_rep4


title: MeCP2_KO_H3K27ac_ChIPseq_rep1


title: MeCP2_WT_H3K27ac_ChIPseq_rep10


title: MeCP2_WT_H3K27ac_ChIPseq_rep8


title: MeCP2_WT_H3K27ac_ChIPseq_rep7


title: MeCP2_WT_H3K27ac_ChIPseq_rep5


title: MeCP2_WT_H3K27ac_ChIPseq_rep6


title: MeCP2_WT_H3K27ac_ChIPseq_rep3


title: MeCP2_KO_H3K36me3_ChIPseq_rep10

description: 10WT_10MeCP2_KO_H3K36me3_ChIPseq_input_gene_body_counts.txt

value: H3K36me3 (Abcam ab9050)


title: MeCP2_WT_H3K27ac_ChIPseq_rep4


title: MeCP2_WT_H3K27ac_ChIPseq_rep1


title: MeCP2_WT_H3K27ac_ChIPseq_rep2


title: MeCP2_KO_H3K27ac_ChIPseq_rep10


title: MeCP2_KO_H3K36me3_ChIPseq_rep9


title: MeCP2_KO_H3K36me3_ChIPseq_rep7


title: MeCP2_KO_H3K36me3_ChIPseq_rep6


title: MeCP2_KO_H3K27ac_ChIPseq_rep6


title: MeCP2_KO_H3K36me3_ChIPseq_rep4


title: MeCP2_KO_H3K36me3_ChIPseq_rep5


title: MeCP2_KO_H3K36me3_ChIPseq_rep3


title: MeCP2_KO_H3K36me3_ChIPseq_rep2


title: MeCP2_KO_H3K27ac_ChIPseq_rep9


title: MeCP2_WT_H3K36me3_ChIPseq_rep10


title: MeCP2_KO_H3K36me3_ChIPseq_rep1


title: MeCP2_WT_H3K36me3_ChIPseq_rep7


title: MeCP2_WT_H3K36me3_ChIPseq_rep8


title: MeCP2_WT_H3K36me3_ChIPseq_rep5


title: MeCP2_WT_H3K36me3_ChIPseq_rep9


title: MeCP2_WT_H3K36me3_ChIPseq_rep4


title: MeCP2_WT_H3K36me3_ChIPseq_rep2


title: MeCP2_WT_H3K36me3_ChIPseq_rep3


title: Dnmt3a_cKO_RNA_rep5

description:
Total RNA
6WT_6Dnmt3a_cKO_visual_cortex_RNAseq_exon_counts.txt

data_processing:
Reads were trimmed with Trimmomatic (v0.36) to remove Illumina adaptors and low quality sequence (settings: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50).
Trimmed reads were mapped to the mm10 Refseq transcriptome and genome using STAR (v2.5.2b) with --outFilterMismatchNoverReadLmax 0.04.
For whole-cell RNA-seq, reads were counted in all exons for each gene using Subread featureCounts (v1.6.0) with default parameters (reversely stranded, multi-mapping reads not counted, multi-overlapping reads not counted). For nuclear and chromatin-associated RNA-seq, reads were counted in the full gene body (TSS to TTS of longest isoform, in order to include intronic reads) using Subread featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Table of raw read counts for exons or gene bodies for all genes.

source_name: Visual cortex

extract_protocol:
Forebrain (cortex and hippocampus) was dissected from 10 8-week-old male MeCP2 knock-out and 10 wild-type littermate controls and 10 8-to-12-week-old male R306C and 10 WT littermate controls and flash frozen. Tissue was removed from dry ice and placed directly into a dounce with 5 mL of Homogenization buffer (HB: 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine KOH pH 7.8, 0.04% BSA, 5 µg/mL Actinomycin D, and RNAsin (Promega)). After 10 strokes with the tight pestle, a 5% Igepal (Sigma) solution in HB was added to a final concentration of 0.32%, followed by five additional strokes with the tight pestle. At this point, 200 μL of lysate was pipetted into a tube with 600 µL Trizol LS (Invitrogen) as the “whole cell” sample. The remaining lysate was filtered first through a 40 μm cell strainer and then through a 20 μm Celltrics filter. Lysate was diluted 1:2 in HB to dilute Igepal to 0.16%, then centrifuged at 500 g for 5 minutes at 4°C. The nuclear pellet was washed twice with 1 mL HB by resuspending and centrifuging at 500 g for 5 minutes at 4°C. Nuclei were resuspended in 1mL HB and 200μL was pipetted into a separate tube, spun at 500 g for 5 minutes at 4°C, and the pellet was resuspended in Trizol as the “nuclear fraction”. The remaining 800 μL was spun at 500 g for 5 minutes at 4°C, then resuspended in 200 μL Glycerol buffer (20 mM Tris pH 8, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.85 mM DTT). 200 μL of Nuclear lysis buffer (1% Igepal, 20 mM Hepes pH 7.5, 300 mM NaCl, 0.2 mM EDTA) was added and nuclei were resuspended, vortexed, and incubated at 4°C for 5 minutes. Chromatin was spun at 16,000 g for 10 minutes at 4°C, and the pellet was resuspended in 800 μL Trizol and homogenized to solubilize. For Dnmt3a cKO mice, visual cortex was dissected and homogenized in Trizol. For all samples, total RNA was chloroform extracted and purified with the Qiagen RNeasy Micro Kit with on-column DNase treatment.
RNA-seq libraries were generated with the NEBNext Ultra Directional Library Prep Kit with rRNA depletion.

value: Female

value: Nestin-cre; Dnmt3a fl/fl

tag: cellular fraction

value: Whole tissue


title: Dnmt3a_cKO_RNA_rep1


title: Dnmt3a_cKO_RNA_rep6


title: MeCP2_KO_H3K36me3_ChIPseq_rep8

value: MeCP2 KO


title: Dnmt3a_cKO_RNA_rep3


title: Dnmt3a_cKO_RNA_rep2


title: Dnmt3a_cKO_RNA_rep4


title: MeCP2_WT_H3K36me3_ChIPseq_rep1


title: Dnmt3a_WT_RNA_rep4

value: Dnmt3a fl/fl


title: Dnmt3a_WT_RNA_rep5


title: Dnmt3a_WT_RNA_rep6


title: Dnmt3a_WT_RNA_rep3


title: Dnmt3a_WT_RNA_rep1


title: Dnmt3a_WT_RNA_rep2


title: R306C_chromatin_associated_RNA_rep10

description:
Chromatin-associated RNA
10WT_10R306C_chromatin_associated_RNAseq_gene_body_counts.txt

value: MeCP2 R306C

value: Chromatin


title: MeCP2_WT_H3K36me3_ChIPseq_rep6


title: R306C_chromatin_associated_RNA_rep9

value: 8-12 weeks


title: R306C_chromatin_associated_RNA_rep7


title: R306C_chromatin_associated_RNA_rep5


title: R306C_chromatin_associated_RNA_rep3


title: R306C_chromatin_associated_RNA_rep4


title: WT_chromatin_associated_RNA_rep10


title: R306C_chromatin_associated_RNA_rep1


title: WT_chromatin_associated_RNA_rep9


title: WT_chromatin_associated_RNA_rep7


title: WT_chromatin_associated_RNA_rep8


title: WT_chromatin_associated_RNA_rep3


title: WT_chromatin_associated_RNA_rep2


title: R306C_nuclear_RNA_rep10

description:
Nuclear RNA
10WT_10R306C_nuclear_RNAseq_gene_body_counts.txt

value: Nuclei


title: WT_chromatin_associated_RNA_rep4


title: R306C_nuclear_RNA_rep8


title: WT_chromatin_associated_RNA_rep5


title: WT_chromatin_associated_RNA_rep1


title: R306C_nuclear_RNA_rep7


title: R306C_nuclear_RNA_rep9


title: R306C_nuclear_RNA_rep6


title: R306C_chromatin_associated_RNA_rep8


title: R306C_nuclear_RNA_rep4


title: R306C_nuclear_RNA_rep5


title: R306C_nuclear_RNA_rep2


title: R306C_chromatin_associated_RNA_rep6


title: R306C_chromatin_associated_RNA_rep2


title: R306C_nuclear_RNA_rep1


title: WT_nuclear_RNA_rep8


title: WT_nuclear_RNA_rep10


title: WT_chromatin_associated_RNA_rep6


title: WT_nuclear_RNA_rep7


title: WT_nuclear_RNA_rep6


title: WT_nuclear_RNA_rep5


title: WT_nuclear_RNA_rep4


title: WT_nuclear_RNA_rep2


title: R306C_whole_cell_RNA_rep9

description:
Total RNA
10WT_10R306C_whole_cell_RNAseq_exon_counts.txt

value: Whole-cell


title: R306C_whole_cell_RNA_rep10

value: Male


title: WT_nuclear_RNA_rep3


title: R306C_whole_cell_RNA_rep8


title: R306C_whole_cell_RNA_rep7


title: WT_nuclear_RNA_rep1


title: R306C_whole_cell_RNA_rep4


title: R306C_whole_cell_RNA_rep3


title: R306C_nuclear_RNA_rep3


title: R306C_whole_cell_RNA_rep6


title: R306C_whole_cell_RNA_rep1


title: R306C_whole_cell_RNA_rep2


title: WT_whole_cell_RNA_rep10


title: WT_whole_cell_RNA_rep9


title: WT_whole_cell_RNA_rep7


title: WT_whole_cell_RNA_rep5


title: WT_whole_cell_RNA_rep4


title: WT_whole_cell_RNA_rep6


title: WT_whole_cell_RNA_rep8


title: WT_nuclear_RNA_rep9


title: WT_whole_cell_RNA_rep3


title: MeCP2_KO_chromatin_associated_RNA_rep8

description:
Chromatin-associated RNA
10WT_10MeCP2_KO_chromatin_associated_RNAseq_gene_body_counts.txt


title: WT_whole_cell_RNA_rep1


title: MeCP2_KO_chromatin_associated_RNA_rep9


title: R306C_whole_cell_RNA_rep5


title: MeCP2_KO_chromatin_associated_RNA_rep7


title: MeCP2_KO_chromatin_associated_RNA_rep6


title: MeCP2_KO_chromatin_associated_RNA_rep5


title: MeCP2_KO_chromatin_associated_RNA_rep2


title: MeCP2_KO_chromatin_associated_RNA_rep4


title: MeCP2_WT_chromatin_associated_RNA_rep10


title: MeCP2_WT_chromatin_associated_RNA_rep9


title: MeCP2_KO_chromatin_associated_RNA_rep1


title: MeCP2_WT_chromatin_associated_RNA_rep8


title: MeCP2_WT_chromatin_associated_RNA_rep6


title: MeCP2_WT_chromatin_associated_RNA_rep7


title: MeCP2_WT_chromatin_associated_RNA_rep5


title: MeCP2_WT_chromatin_associated_RNA_rep3


title: MeCP2_WT_chromatin_associated_RNA_rep4


title: WT_whole_cell_RNA_rep2


title: MeCP2_WT_chromatin_associated_RNA_rep1


title: MeCP2_WT_chromatin_associated_RNA_rep2


title: MeCP2_KO_nuclear_RNA_rep9

description:
Nuclear RNA
10WT_10MeCP2_KO_nuclear_RNAseq_gene_body_counts.txt


title: MeCP2_KO_nuclear_RNA_rep8


title: MeCP2_KO_nuclear_RNA_rep10


title: MeCP2_KO_nuclear_RNA_rep6


title: MeCP2_KO_chromatin_associated_RNA_rep10


title: MeCP2_KO_nuclear_RNA_rep5


title: MeCP2_KO_chromatin_associated_RNA_rep3


title: MeCP2_KO_nuclear_RNA_rep4


title: MeCP2_KO_nuclear_RNA_rep1


title: MeCP2_KO_nuclear_RNA_rep2


title: MeCP2_KO_nuclear_RNA_rep3


title: MeCP2_WT_nuclear_RNA_rep10


title: MeCP2_WT_nuclear_RNA_rep8


title: MeCP2_WT_nuclear_RNA_rep6


title: MeCP2_WT_nuclear_RNA_rep7


title: MeCP2_WT_nuclear_RNA_rep4


title: MeCP2_WT_nuclear_RNA_rep5


title: MeCP2_KO_nuclear_RNA_rep7


title: MeCP2_WT_nuclear_RNA_rep2


title: MeCP2_WT_nuclear_RNA_rep3


title: MeCP2_WT_nuclear_RNA_rep1


title: MeCP2_KO_whole_cell_RNA_rep6

description:
Total RNA
10WT_10MeCP2_KO_whole_cell_RNAseq_exon_counts.txt


title: MeCP2_KO_whole_cell_RNA_rep8


title: MeCP2_KO_whole_cell_RNA_rep7


title: MeCP2_KO_whole_cell_RNA_rep10


title: MeCP2_KO_whole_cell_RNA_rep4


title: MeCP2_KO_whole_cell_RNA_rep3


title: MeCP2_WT_whole_cell_RNA_rep9


title: MeCP2_WT_whole_cell_RNA_rep10


title: MeCP2_KO_whole_cell_RNA_rep5


title: MeCP2_KO_whole_cell_RNA_rep1


title: MeCP2_WT_whole_cell_RNA_rep7


title: MeCP2_WT_nuclear_RNA_rep9


title: MeCP2_WT_whole_cell_RNA_rep8


title: MeCP2_WT_whole_cell_RNA_rep6


title: MeCP2_WT_whole_cell_RNA_rep4


title: MeCP2_WT_whole_cell_RNA_rep5


title: MeCP2_WT_whole_cell_RNA_rep3


title: MeCP2_WT_whole_cell_RNA_rep2


title: MeCP2_WT_whole_cell_RNA_rep1


title: MeCP2_KO_whole_cell_RNA_rep2


title: MeCP2_KO_whole_cell_RNA_rep9


title: MeCP2_KO_BS_rep2

data_processing:
Reads were mapped to the mm10 genome using BSmap (Xi and Li, 2009).
Duplicate reads were removed and only uniquely mapping reads were kept.
Genome_build: mm10
Supplementary_files_format_and_content: Each line contains a CA or CG in the genome with the following information: chromosome, strand, nucleotide position, number of non-converted base-calls at this position (#C), total number of reads for the base at this position (# of C and T base-calls).

extract_protocol:
Genomic DNA was extracted from 8-week-old MeCP2 KO and WT forebrain with the Qiagen DNeasy kit and sonicated to 200 bp with a Covaris M220.
OxBS-seq libraries were generated as described in (Stroud et al., 2017). DNA was ligated to NEXTflex methylated adapters (Bioo Scientific). Bisulfite conversions and oxidation reactions were performed using the TrueMethyl oxBS-seq kit following the manufacturer instructions (Cambridge Epigenetix). Half of the sample was used for BS-seq without oxidation treatment, and half the sample was used for oxBS-seq as recommended by the manufacturer.

tag: library type

value: BS-seq


title: MeCP2_KO_OX_rep1

value: oxBS-seq


title: MeCP2_WT_OX_rep3

value: WT


title: MeCP2_WT_OX_rep2


title: MeCP2_KO_OX_rep2


title: MeCP2_KO_OX_rep3


title: MeCP2_WT_OX_rep1


title: MeCP2_WT_BS_rep3


title: MeCP2_WT_BS_rep1


title: MeCP2_KO_BS_rep1


title: scRNA_ILCs_nippo_lung_day14

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

data_processing:
Sequence reads from all samples were processed and aggregated using Cell Ranger.
Genome_build: mm10

source_name: mouse primary lung ILCs

growth_protocol: scRNAseq ex vivo: 1.3 x 10^4 Lin- CD3- TCRβ- Thy1+ ILCs or CD3+ TCRb+ CD4+ Th cells were purified from lungs of mice by cell sorting (>98% purity; FACSAria III or FACSAria Fusion; Becton Dickinson) and immediately pocessed for subsequent scRNA-seq (10X Genomics).

extract_protocol:
Freshly sorted ILCs and Th cells (13,000 cells each) were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).
Indexed libraries were multiplexed and sequenced on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.

value: female

value: 6-12 weeks

tag: culture condition

value: ex vivo (growth protocol 2)

tag: exp id

tag: lab  data id


title: scRNA_ILCs_nippo_lung_day2


title: scRNA_ILCs_nippo_lung_day5


title: scRNA_ILCs_lung_steady


title: scRNA_CD4_T_nippo_lung_day9

source_name: mouse primary lung Th cells


title: scRNA_ILCs_nippo_lung_day9


title: scRNA_CD4_T_nippo_lung_day5


title: scRNA_CD4_T_nippo_lung_day14


title: Dnmt3a_Input_WT4

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

data_processing:
Sequenced reads were mapped to the mm9 genome using bowtie2 alignment, and reads were deduplicated to consolidate PCR duplicate reads. Deduplicated reads were used to quantify read density normalized by the number of reads per sample and by read length in basepairs. Bedtools coverage –counts was used to quantify ChIP signal at the transcriptional start site (TSS), gene body (GB), and transcriptional end site (TES). For consistency with methylation analysis, the TSS was defined as a 1kb region surrounding the TSS (+/-500bp), the GB was defined as 3kb downstream of the TSS to the end of the transcript, and the TES was defined as 2kb upstream through 3kb downstream of the end of the transcript. edgeR was then used to determine differential ChIP-signal across genotypes.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated table (with header) of H3K27ac peaks, identifiers, various peak-associated ChIP signals, and methylation information

source_name: Cortex

growth_protocol: Brain tissue was taken from MeCP2 knockout, overexpression and wild-type mice maintained under standard housing conditions.

extract_protocol:
Cerebral cortex was dissected on ice in phosphate buffered saline from 1) MeCP2 knockout and wild-type male litter mates at 7-8 weeks old and 2) MeCP2 overexpression and wild-type male litter mates at 7-10 weeks old. The tissue was flash-frozen in liquid nitrogen and stored at -80°C. ChIP experiments were performed on half a cortex as previously described (Cohen et al., 2011), using an alternative chromatin fragmentation method. Chromatin were fragmented with Covaris E220 sonicator (5% Duty Factory, 140 Peak Incidence Power, 200 cycles per burst, milliTUBE 1mL AFA Fiber). ChIP was performed with H3K27ac (Abcam ab4729), H3K4me3 (Abcam ab1012), H3K36me3 (Active Motif 61101), and MeCP2 (rabbit polyclonal (Chen et al., 2003)).
ChIP libraries for H3K27ac, H3K4me3, and H3K36me3 were generated using Ovation Ultralow Library System V2 (NuGEN) and libraries for MeCP2 with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences).
Libraries were pooled to a final concentration of 8-10nM and sequenced using Illumina HiSeq 3000 with GTAC, yielding 15-20 million single-end reads per sample.

value: wild type

tag: Sex

value: 7-8 weeks


title: Dnmt3a_Input_cKO2

value: Dnmt3a conditional knock out


title: MeCP2_KO_BS_rep3

value: 8 weeks

value: MeCP2 KO


title: scRNA_CD4_T_lung_steady


title: MeCP2_WT_BS_rep2


title: Dnmt3a_H3K27ac_WT9

value: Female


title: Dnmt3a_Input_cKO4


title: Dnmt3a_H3K27ac_cKO4


title: Dnmt3a_H3K27ac_WT7


title: Dnmt3a_H3K27ac_cKO2


title: Dnmt3a_H3K27ac_WT4


title: Dnmt3a_H3K27ac_cKO3


title: Dnmt3a_H3K27ac_WT_4862


title: Dnmt3a_WT_4121_bs

data_processing:
Raw FASTQ files were trimmed with Trim Galore, using a quality filter of 20, then rRNA sequences were filtered out using Bowtie, using rRNA sequences from Mus Musculus obtained from the NCBI sequence database (see Key Resources Table). The unaligned reads from this step were then aligned to mm9 using STAR (Dobin et al., 2013), using the default parameters. Reads mapping to multiple regions in the genome were then filtered out, and uniquely mapping reads were converted to BED files. Intronic and exonic reads were then separated. To do this, splice-site reads were first filtered out of the BED read files, then reads that mapped entirely within exons were added to the splice-site reads to make the exonic read file. All remaining reads that overlapped introns were considered intronic reads. Finally, reads were assigned to genes using bedtools coverage -counts.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file of all Cs in the genome covered at least once in the sample. 4th column gives the context of the methyl base, 5th column is the number of Cs mapping to C (indicating a methylated base) at that position, and the 6th column is the number of bases mapping to Cs or Ts (representing coverage).

source_name: Cortex nucleus

growth_protocol: Brain tissue was taken from MeCP2 knockout, overexpression, and wild-type mice maintained under standard housing conditions.

extract_protocol:
Cerebral cortex 7-10 weeks of age was dissected on ice in phosphate buffer saline. The tissue was flash-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from 1/16th of a whole cortex using RLT buffer following RNeasy Micro Kit (Qiagen). Nuclear RNA was isolated following a modified version of the protocol described by Mo et al., 2015. Briefly, half of a cortex was homogenized in 0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH using a glass dounce homogenizer. Nuclei were isolated via centrifugation at 10,000g for 18 minutes at 4°C (Sorvall HB-4) by pelleting through a 30% iodixanol density gradient (Sigma D1556). RNA was isolated from nuclei by resuspending pellet in RLT buffer following the RNeasy Micro Kit (Qiagen).
RNA libraries were generated from 250ng total and nuclear RNA with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) using a modified amplification protocol (37°C, 15 minutes; 98°C, 30 seconds; (98°C, 10 seconds; 65°C, 30 seconds; 72°C, 30 seconds)x13; 72°C, 5 minutes; 4°C hold. RNA libraries were pooled at a final concentration of 8-10nM
RNA was sequenced using Illumina HiSeq 2500 or 3000 with the Genome Technology Access Center (GTAC) at Washington University in St. Louis, typically yielding 20-30 million single-end reads per sample.


title: Dnmt3a_WT_4963_bs


title: Dnmt3a_WT_72_bs


title: scRNA_CD4_T_nippo_lung_day2


title: Dnmt3a_WT_7_bs


title: Dnmt3a_H3K27ac_cKO_4755


title: TGWT_TG3_cell

data_processing:
Raw FASTQ files were trimmed with Trim Galore, using a quality filter of 20, then rRNA sequences were filtered out using Bowtie, using rRNA sequences from Mus Musculus obtained from the NCBI sequence database (see Key Resources Table). The unaligned reads from this step were then aligned to mm9 using STAR (Dobin et al., 2013), using the default parameters. Reads mapping to multiple regions in the genome were then filtered out, and uniquely mapping reads were converted to BED files. Intronic and exonic reads were then separated. To do this, splice-site reads were first filtered out of the BED read files, then reads that mapped entirely within exons were added to the splice-site reads to make the exonic read file. All remaining reads that overlapped introns were considered intronic reads. Finally, reads were assigned to genes using bedtools coverage -counts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated table (with header) of genes, identifiers, and various gene-associated RNA coverage, methylation level, and ChIP signal

source_name: Cortex whole cell

value: MeCP2 overexpression

value: FVB

value: 7-10 weeks


title: TGWT_TG2_cell


title: Dnmt3a_WT_9_bs


title: TGWT_TG1_cell


title: Dnmt3a_WT_6_bs


title: TGWT_TG5_cell


title: TGWT_WT5_cell


title: TGWT_TG4_cell


title: Dnmt3a_Input_WT2


title: Dnmt3a_H3K27ac_cKO9


title: TGWT_WT2_cell


title: TGWT_WT3_cell


title: TGWT_WT1_cell


title: Dnmt3a_H3K27ac_WT2


title: KOWT_KO6_cell

value: MeCP2 knock out


title: TGWT_WT4_cell

value: Male


title: KOWT_KO5_cell


title: KOWT_KO1_cell


title: KOWT_WT4_cell


title: KOWT_KO4_cell


title: KOWT_KO3_cell


title: KOWT_WT5_cell


title: WTTG_Input_Tg3

data_processing:
Sequenced reads were mapped to the mm9 genome using bowtie2 alignment, and reads were deduplicated to consolidate PCR duplicate reads. Deduplicated reads were used to quantify read density normalized by the number of reads per sample and by read length in basepairs. Bedtools coverage –counts was used to quantify ChIP signal at the transcriptional start site (TSS), gene body (GB), and transcriptional end site (TES). For consistency with methylation analysis, the TSS was defined as a 1kb region surrounding the TSS (+/-500bp), the GB was defined as 3kb downstream of the TSS to the end of the transcript, and the TES was defined as 2kb upstream through 3kb downstream of the end of the transcript. edgeR was then used to determine differential ChIP-signal across genotypes.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated table (with header) of H3K27ac peaks, identifiers, and various peak-associated ChIP signals, and methylation information


title: WTTG_Input_WT3


title: WTTG_H3K4me3_Tg3


title: WTTG_H3K27ac_Tg3


title: KOWT_WT1_cell


title: WTTG_H3K4me3_WT3


title: WTTG_H3K36me3_Tg3


title: KOWT_WT3_cell


title: WTTG_H3K27ac_WT2


title: WTTG_H3K36me3_WT3


title: WTTG_H3K27ac_WT3


title: WTTG_H3K27ac_Tg2


title: WTTG_H3K4me3_Tg1


title: WTTG_Input_Tg1


title: WTTG_H3K27ac_WT1


title: WTTG_H3K36me3_WT1


title: WTTG_Input_WT1


title: WTTG_H3K36me3_Tg1


title: WTKO_H3K27ac_WT8


title: KOWT_WT6_cell


title: WTKO_H3K4me3_KO6


title: WTTG_H3K4me3_WT1


title: WTKO_H3K4me3_WT6


title: WTKO_H3K27ac_KO8


title: WTKO_H3K27ac_WT6


title: WTKO_H3K27ac_KO6


title: WTKO_H3K4me3_KO3


title: WTKO_H3K36me3_KO3


title: WTKO_H3K4me3_WT3


title: WTKO_Input_WT3


title: WTKO_Input_KO3


title: WTKO_H3K36me3_WT3


title: WTKO_H3K27ac_WT3


title: WTKO_H3K36me3_KO2


title: WTKO_H3K27ac_KO2


title: WTKO_H3K27ac_KO3


title: WTKO_H3K36me3_WT2


title: WTTG_H3K27ac_Tg1


title: WTKO_H3K36me3_KO1


title: WTKO_Input_WT2


title: WTKO_H3K27ac_WT2


title: WTKO_H3K36me3_WT1


title: WTKO_Input_KO1


title: WTKO_H3K27ac_WT1


title: WTKO_Input_KO2


title: WTKO_H3K27ac_KO1


title: WTKO_Input_WT1


title: WTKO_H3K36me3_WT6


title: WTKO_H3K36me3_KO6


title: WTKO_H3K4me3_KO2


title: D06_M82_TRAP_ele-25 (TRAP-Seq)

city: Davis

first: Siobhan

last: Brady

state: CA

address: 451 Health Sciences Drive, 4303 GBSF

department: GBSF

institute: UC Davis

description:
TRAP_RawGeneCounts.csv
SG-TRAP-25_S32_L005_R1_001

data_processing:
Library strategy: TRAP-seq
Before and after read processing, libraries were analyzed with FastQC.
Barcodes were trimmed using fastx_trimmer (-f 9 -v -Q 33) and further quality trimmed/adapter removal was done with reaper (-geom no-bc -dust-suffix-late 10/ACTG -dust-suffix 10/ACTG --noqc -nnn-check 1/1 -qqq-check 33/10 -clean-length 30 -tri 20 -polya 5 --bcq-late)
Trimmed reads were mapped to the reference transcriptome of S. lycopersicum (v3.2) using bowtie with subsequent conversion to BAM format using samtools.
HTSeq-count was used to obtain raw counts
Differential expression was assessed with limma-voom using the voomWithQualityWeights() function.
Genome_build: ITAG3.2 (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.2_release/ITAG3.2_cDNA.fasta)
Supplementary_files_format_and_content: comma separated files (one for RNA-Seq another for TRAP-Seq data) with raw counts for each sample (RNASeq tech reps are unaggregated).

organism: Solanum lycopersicum

source_name: shoot

growth_protocol: Seeds were sterilized and sown in Profile calcined Clay media in 4-inch pots with a modified removable bottom. Plants were grown in Conviron  392 PGR15 growth chambers (Controlled Environments Ltd., Winnipeg, Manitoba, Canada).

extract_protocol:
For transcriptome profiling, root tissue from three individual plants was pooled together to yield one root sample per treatment-species combination per day on each of the three sampling days, and shoot tissue from the same three plants was pooled together to yield one shoot sample per treatment-species combination per day on each of the three sampling days.
RNAseq Library Preparation   RNAseq libraries were prepared using the method described by (Kumar et al., 2012). Briefly, for each library, the pooled root or shoot samples were homogenized in lysis and binding buffer containing beta-mercaptoethanol. Tissue was disrupted using a mortar and pestle and a Mini-beadbeater-96 high-throughput cell disruptor (BioSpec Products, Bartlesville, OK). Oligo (dT)25-coated Dynabeads (Ambion, Foster City, CA) were then added to the lysate, and mixed for 10 minutes to allow oligo (dT) beads to hybridize to poly-adenylated mRNA. cDNA was then synthesized and digested to ~300 bp fragments using NEBNext DNA fragmentase enzyme mix (NEB, Beverly, MA, USA). Library fragments greater than 300 bp were purified using Ampure XP solid phase reverse immobilization (SPRI) magnetic beads (Agencourt Bioscience, Beverly, MA, USA). For each library, one of the ninety-six unique barcoded adapters described in Kumar et al (2012) was ligated to each library, enabling multiplexing. cDNA was quantified using a SYBR-green based method on a plate reader, libraries were pooled, and fragment size and quality was checked using a BioAnalyzer (Agilent Technologies, Santa Clara, CA).  Translating Ribosome Affinity Purification (TRAP)   To determine the effects of eCO2 on the translatome of shoot tissue, transgenic S. lycopersicum and S. pennellii expressing a FLAG-epitope on the ribosomal L18 (RPL18) under the 35S promoter (Ron et al., 2013) were grown in ambient and elevated [CO2] in the same conditions and chambers as described above. At 6 and 12 DAP, tissue was collected for the Translating Ribosome Affinity Purification (TRAP) protocol. Because the biomass of plant tissues in young seedlings was small, and because the TRAP populations were segregating, we pooled multiple plants (up to 15) together to ensure that adequate mRNA for library preparation could be collected via the ribosomal pulldown.   The TRAP procedure has been described by (Zanetti et al., 2005). Briefly, tissues from transgenic plants expressing the FLAG epitope was ground in liquid nitrogen using a mortar and pestle, and homogenized in polysome extraction buffer. Samples were clarified by centrifugation and filtration through Miracloth, and clarified extract was added to magnetic beads that were coated in anti-flag antibody. Beads and extract were incubated at 4˚C using a nutator for 2 hours, and washed 6-7 times with wash buffer. Polysomes bound to magnetic beads were then frozen at -80°C until RNAseq library preparation.   RNAseq libraries were prepared from TRAP polysomes using the method described by (Townsley et al., 2015). Lysis and binding buffer containing beta-mercaptoethanol was added to anti-flag magnetic beads and bound ribosomes, allowing elution of mRNA. mRNA was then hybridized to biotin-20nt-dT oligos, allowing pulldown of mRNA out of solution with the use of magnetic streptavidin beads. mRNA was then washed with three successive buffers, eluted off of beads at 80˚C, and a secondary wash was performed, by adding more biotin-20nt-dT oligos to the mRNA, repeating the bead pulldown, and the buffer washes. mRNA was then heat-fragmented, and first and second strand cDNA was synthesized. The optimal fragment size was selected using Ampure beads, and libraries were enriched using PCR.

treatment_protocol: Chambers were set at either ambient (400 ppm) or eCO2 (700 ppm), 325 μmol m-2 s-1 PPFD, 70% Relative humidity, 16:8 light: dark schedule, and 22° C at the Controlled Environment Facility at University of California, Davis. Plants were watered every 2-3 days with 40% Long-Ashton solution containing 6 mM NH4NO3. The location of flats within each chamber and the location of plants within each flat were rotated upon every watering, and CO2 treatment assignments were rotated between chambers at every experimental replication in order to avoid any experimental artifacts caused by differences between chambers.

tag: cultivar

value: ele

tag: day

tag: r

tag: pool

tag: lnrep

tag: tissue

value: shoot


title: D06_M82_TRAP_ele-26 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-26_S33_L005_R1_001


title: D12_M82_TRAP_amb-30 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-30_S37_L005_R1_001

value: amb


title: D12_M82_TRAP_amb-29 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-29_S36_L005_R1_001


title: D12_M82_TRAP_amb-24 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-24_S31_L005_R1_001


title: D12_M82_TRAP_amb-23 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-23_S30_L005_R1_001


title: D12_M82_TRAP_ele-18 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-18_S25_L005_R1_001


title: D12_M82_TRAP_ele-17 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-17_S24_L005_R1_001


title: D06_M82_TRAP_amb-13 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-13_S20_L005_R1_001


title: D12_M82_TRAP_ele-12 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-12_S19_L005_R1_001


title: D06_M82_TRAP_amb-14 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-14_S21_L005_R1_001


title: D12_M82_TRAP_ele-11 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-11_S18_L005_R1_001


title: D06_M82_TRAP_ele-04 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-04_S11_L005_R1_001


title: D06_M82_TRAP_ele-03 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-03_S10_L005_R1_001


title: D06_M82_TRAP_amb-07 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-07_S14_L005_R1_001


title: R5_D12_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_M82_shoot_Pool2_LnRep4.fq.gz

data_processing:
Before and after read processing, libraries were analyzed with FastQC.
Barcodes were trimmed using fastx_trimmer (-f 9 -v -Q 33) and further quality trimmed/adapter removal was done with reaper (-geom no-bc -dust-suffix-late 10/ACTG -dust-suffix 10/ACTG --noqc -nnn-check 1/1 -qqq-check 33/10 -clean-length 30 -tri 20 -polya 5 --bcq-late)
Trimmed reads were mapped to the reference transcriptome of S. lycopersicum (v3.2) using bowtie with subsequent conversion to BAM format using samtools.
HTSeq-count was used to obtain raw counts
Differential expression was assessed with limma-voom using the voomWithQualityWeights() function.
Genome_build: ITAG3.2 (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.2_release/ITAG3.2_cDNA.fasta)
Supplementary_files_format_and_content: comma separated files (one for RNA-Seq another for TRAP-Seq data) with raw counts for each sample (RNASeq tech reps are unaggregated).


title: D06_M82_TRAP_amb-08 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-08_S15_L005_R1_001


title: R5_D12_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R5_D12_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_M82_shoot_Pool2_LnRep3.fq.gz


title: R5_D12_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_M82_root_Pool2_LnRep3.fq.gz

source_name: root

value: root


title: R5_D12_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R5_D12_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_M82_root_Pool2_LnRep4.fq.gz


title: R5_D12_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_M82_root_Pool2_LnRep1.fq.gz


title: R5_D12_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_M82_root_Pool1_LnRep1.fq.gz


title: WTKO_H3K4me3_WT2

tag: strain

tag: age


title: R5_D12_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_M82_root_Pool2_LnRep2.fq.gz


title: R5_D12_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: R5_D12_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R5_D12_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_M82_root_Pool2_LnRep2.fq.gz


title: R5_D12_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: R5_D12_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_M82_root_Pool2_LnRep4.fq.gz


title: R5_D12_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_M82_root_Pool2_LnRep1.fq.gz


title: R5_D12_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: R5_D12_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_M82_root_Pool1_LnRep1.fq.gz


title: R5_D12_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_M82_root_Pool2_LnRep3.fq.gz


title: R5_D09_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_M82_shoot_Pool2_LnRep3.fq.gz


title: R5_D12_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: R5_D09_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R5_D09_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R5_D09_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_M82_root_Pool2_LnRep4.fq.gz


title: R5_D09_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: R5_D09_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_M82_root_Pool2_LnRep1.fq.gz


title: R5_D09_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_M82_root_Pool2_LnRep3.fq.gz


title: R5_D09_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_M82_root_Pool2_LnRep2.fq.gz


title: R5_D09_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: R5_D09_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: R5_D09_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_M82_root_Pool1_LnRep1.fq.gz


title: R5_D09_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R5_D12_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R5_D09_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R5_D09_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_M82_root_Pool2_LnRep2.fq.gz


title: R5_D09_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_M82_root_Pool2_LnRep3.fq.gz


title: R5_D09_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_M82_root_Pool2_LnRep4.fq.gz


title: R5_D09_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: R5_D09_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_M82_root_Pool2_LnRep1.fq.gz


title: R5_D06_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_M82_shoot_Pool2_LnRep4.fq.gz


title: R5_D06_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R5_D06_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_M82_shoot_Pool2_LnRep3.fq.gz


title: R5_D09_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_ele_M82_shoot_Pool2_LnRep4.fq.gz


title: R5_D09_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D09_amb_M82_root_Pool1_LnRep1.fq.gz


title: R5_D06_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_M82_root_Pool2_LnRep4.fq.gz


title: R5_D06_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R5_D06_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: R5_D06_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_M82_root_Pool2_LnRep3.fq.gz


title: R5_D06_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_M82_root_Pool2_LnRep1.fq.gz


title: R5_D06_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_M82_root_Pool2_LnRep2.fq.gz


title: R5_D06_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R5_D06_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_M82_root_Pool2_LnRep1.fq.gz


title: R5_D06_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: R5_D06_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: R5_D06_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: R5_D06_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_M82_root_Pool2_LnRep4.fq.gz


title: R4_D12_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R4_D12_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_M82_shoot_Pool2_LnRep3.fq.gz


title: R5_D06_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_M82_root_Pool2_LnRep3.fq.gz


title: R4_D12_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_M82_shoot_Pool2_LnRep4.fq.gz


title: R4_D12_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R5_D06_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R4_D12_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_M82_root_Pool2_LnRep4.fq.gz


title: R5_D06_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_amb_M82_root_Pool1_LnRep1.fq.gz


title: R4_D12_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: R4_D12_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_M82_root_Pool2_LnRep3.fq.gz


title: R5_D06_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_M82_root_Pool2_LnRep2.fq.gz


title: R4_D12_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_M82_root_Pool2_LnRep2.fq.gz


title: R5_D06_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D06_ele_M82_root_Pool1_LnRep1.fq.gz


title: R4_D12_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_M82_root_Pool1_LnRep1.fq.gz


title: R4_D12_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: R4_D12_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: R4_D12_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_ele_M82_root_Pool2_LnRep1.fq.gz


title: R4_D12_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_M82_root_Pool2_LnRep4.fq.gz


title: R4_D12_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R4_D12_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: R4_D12_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_M82_root_Pool2_LnRep3.fq.gz


title: R4_D12_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_M82_root_Pool2_LnRep2.fq.gz


title: R4_D09_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R4_D12_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_M82_root_Pool2_LnRep1.fq.gz


title: R4_D12_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_M82_root_Pool1_LnRep1.fq.gz


title: R4_D09_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R4_D09_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_M82_shoot_Pool2_LnRep3.fq.gz


title: R4_D09_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R4_D09_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: R4_D09_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: R4_D09_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_M82_root_Pool2_LnRep2.fq.gz


title: R4_D09_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_M82_root_Pool1_LnRep1.fq.gz


title: R4_D09_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_M82_root_Pool2_LnRep4.fq.gz


title: R4_D09_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R4_D09_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: R4_D09_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: R4_D09_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_M82_root_Pool2_LnRep3.fq.gz


title: R4_D12_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D12_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R4_D09_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_M82_root_Pool2_LnRep2.fq.gz


title: R4_D09_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_M82_root_Pool2_LnRep1.fq.gz


title: R4_D09_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_M82_root_Pool1_LnRep1.fq.gz


title: R4_D06_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_M82_shoot_Pool2_LnRep3.fq.gz


title: R4_D06_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_M82_shoot_Pool2_LnRep4.fq.gz


title: R4_D06_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R4_D06_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: R4_D09_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_M82_shoot_Pool2_LnRep4.fq.gz


title: R4_D09_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_M82_root_Pool2_LnRep3.fq.gz


title: R4_D09_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_ele_M82_root_Pool2_LnRep1.fq.gz


title: R4_D06_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_M82_root_Pool2_LnRep4.fq.gz


title: R4_D06_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R4_D09_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D09_amb_M82_root_Pool2_LnRep4.fq.gz


title: R4_D06_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_M82_root_Pool2_LnRep1.fq.gz


title: R4_D06_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_M82_root_Pool2_LnRep3.fq.gz


title: R4_D06_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_M82_root_Pool1_LnRep1.fq.gz


title: R4_D06_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R4_D06_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_M82_root_Pool2_LnRep3.fq.gz


title: R4_D06_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: R4_D06_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: R4_D06_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R4_D06_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_M82_root_Pool2_LnRep4.fq.gz


title: R4_D06_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_M82_root_Pool2_LnRep2.fq.gz


title: R4_D06_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_M82_root_Pool1_LnRep1.fq.gz


title: R4_D06_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_M82_root_Pool2_LnRep1.fq.gz


title: R3_D12_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_M82_shoot_Pool2_LnRep4.fq.gz


title: R3_D12_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R3_D12_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R3_D12_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_M82_shoot_Pool2_LnRep3.fq.gz


title: R3_D12_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: R3_D12_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_M82_root_Pool1_LnRep1.fq.gz


title: R3_D12_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_M82_root_Pool2_LnRep2.fq.gz


title: R3_D12_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_M82_root_Pool2_LnRep1.fq.gz


title: R3_D12_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: R3_D12_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_M82_root_Pool2_LnRep3.fq.gz


title: R4_D06_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_ele_M82_root_Pool2_LnRep2.fq.gz


title: R3_D12_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: R4_D06_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R4_D06_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: R3_D12_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R3_D12_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R3_D12_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: R3_D12_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_M82_root_Pool2_LnRep3.fq.gz


title: R3_D12_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_M82_root_Pool2_LnRep2.fq.gz


title: R3_D12_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_M82_root_Pool2_LnRep4.fq.gz


title: R3_D12_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_M82_root_Pool2_LnRep1.fq.gz


title: ATAC-seq replicate 3 ("P15-1")

city: New Haven

first: James

middle: Patrick

last: Noonan

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description:
ATAC_rep3
P15-1_peaks.bb
P15-1_treat_pileup.bw
hNSC_50_peaks.bb
hNSC_50_treat_pileup.bw

data_processing:
Basecalling performed with CASSAVA
Inert library reads were trimmed using fastx_trimmer (options -Q 33 -f 10) and read pais were aligned using PEAR (option -q 33). Adapter sequences were trimmed using Cutadapt, first the adapters on either side of the construct and finally the construct consisting of enhancer fragment-adapter-barcode tag was split at the adapter into fragment and adapter (option -e 0.16). Fragment sequences were aligned to the fragment library using Bowtie2.
Competent library and experimental MPRA reads containing barcode tags were trimmed using fastx_trimmer (options -Q 33 -l 133 (read 1) -l 126 (read 2) and read pairs were aligned using PEAR (option -q 33). Adapter sequences were trimmed using Cutadapt (option -e 0.16).
ATAC-seq reads were mapped using Bowtie2 (option -X 2000). Reads mapping to the mitochondrion or to ENCODE-defined black listed regions were removed. Peaks were called with MACS2 (options -B --nomodel --shift -25 --extsize 50).
Genome_build: GRCh37/hg19 (ATAC-seq)
Supplementary_files_format_and_content: MPRA count files contain raw counts of MPRA reads mapped to their barcode tag and fragment of origin plus annotations.

organism: Homo sapiens

source_name: Neural Stem Cells

growth_protocol: Neural stem cells were grown in DMEM/F12 with GlutaMAX, StemPro Neural Supplement, bFGF, EGF added in flasks coated with Matrigel at 37°C and 5% CO2. Cells were passaged using Accutase every 48 hours.

extract_protocol:
Inert and competent libraries were sequenced from plasmid PCR amplicons. Experimental libraries were extracted from NSCs using Qiagen Allprep and MinElute PCR Purification kits (pDNA, 5% of each sample) and Qiagen RNeasy Mini kit (cDNA, 95%). cDNA was synthesized using Invitrogen SuperScript III reverse transcription kit and using a mixture between a custom, library-specific primer and oligo-dT primers (MPRA1) or only custom primer (MPRA2).
We amplfied the library amplicon using qRT-PCR to stop amplification in the exponential phase. pDNA and cDNA libraries were then paired-end sequenced for 150 cycles on an Illumina HiSeq 4000s (MPRA1) or NovaSeq 6000s (MPRA2), including 5% phi-X spike-in.

treatment_protocol: MPRA libraries were transfected using a Lonza Nucleofector 2b and grown for 6 hours post transfection.

tag: cell type

value: H9-derived Neural Stem Cells

tag: passage


title: R3_D12_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_amb_M82_root_Pool1_LnRep1.fq.gz


title: R3_D09_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_M82_shoot_Pool2_LnRep4.fq.gz


title: R3_D09_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_M82_shoot_Pool2_LnRep3.fq.gz


title: R3_D09_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: R3_D12_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D12_ele_M82_root_Pool2_LnRep4.fq.gz


title: ATAC-seq replicate 1 ("P5-1")

description:
ATAC_rep1
P5-1_peaks.bb
P5-1_treat_pileup.bw
hNSC_50_peaks.bb
hNSC_50_treat_pileup.bw


title: R3_D09_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_M82_root_Pool2_LnRep2.fq.gz


title: ATAC-seq replicate 2 ("P5-2")

description:
ATAC_rep2
P5-2_peaks.bb
P5-2_treat_pileup.bw
hNSC_50_peaks.bb
hNSC_50_treat_pileup.bw


title: R3_D09_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_M82_root_Pool2_LnRep4.fq.gz


title: R3_D09_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_M82_root_Pool2_LnRep1.fq.gz


title: R3_D09_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_M82_root_Pool1_LnRep1.fq.gz


title: CENP-T Cut&Run-seq untreated

city: Paris

first: Riccardo

last: Gamba

address: 12 rue Lhomond

country: France

institute: Insitut Curie

source_name: Retina, eye; pigmented epithelium

growth_protocol: 37 ° 5%CO2 DMEM/F12 medium with 10% FBS 0.123% Sodium Bicarbonate 100U/mL penicillin 100U/mL streptomycin 2mM L-glutamine

extract_protocol:
according to the CUT&RUN protocol reported by Skene and Henikoff, eLife, 2017
Illumina TruSeq ChIP Library Preparation Kit

tag: cell line

tag: immortalization

value: hTERT immortalized

value: retina

tag: molecule subtype

value: enriched DNA


title: CENP-T Cut&Run-seq auxin

description: Cells were treated with auxin analog IAA for 8 hours before Cut&Run


title: D12_penn_TRAP_ele-32 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-32_S39_L005_R1_001

organism: Solanum pennellii


title: WGS

source_name: Dukes' type C, colorectal adenocarcinoma

value: colon

value: genomic DNA


title: R3_D09_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R3_D09_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: R3_D09_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R3_D09_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: D12_penn_TRAP_ele-31 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-31_S38_L005_R1_001


title: R3_D09_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R3_D09_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_M82_root_Pool2_LnRep4.fq.gz


title: R3_D09_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: D06_penn_TRAP_amb-28 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-28_S35_L005_R1_001


title: CENP-C Cut&Run-seq


title: R3_D09_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_ele_M82_root_Pool2_LnRep3.fq.gz


title: R3_D09_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: R3_D09_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_M82_root_Pool2_LnRep3.fq.gz


title: R3_D09_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_M82_root_Pool2_LnRep2.fq.gz


title: D06_penn_TRAP_amb-27 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-27_S34_L005_R1_001


title: R3_D09_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_M82_root_Pool2_LnRep1.fq.gz


title: D12_penn_TRAP_ele-22 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-22_S29_L005_R1_001


title: IP_CENPA_shb

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

data_processing:
To identify putative centromeric transcripts from the RIP-seq results, we followed a computational pipeline as described in Quenet, et al., (2016) Methods Enzymol, 573, 445-466. Briefly, raw reads in fastq format were cropped to remove low quality base calls from read ends with Trimmomatic (Bolger et al., 2014). These pre-processed reads were then used in a first pass alignment to the repeating rDNA subunit (U13369.1, retrieved from GenBank) with Bowtie2 (Langmead et al., 2012) in sensitive mode, to deplete ribosomal transcripts in silico. The unaligned reads from this process were used for further analysis. These reads were mapped to the Build 38 reference genome (hg38) using Tophat (Trapnell et al., 2012). The centromeric sequence included in this version of the reference allowed us to map reads deriving from centromeric transcripts. Libraries for SW480 samples and replicates 3 and 4 of HeLa were trimmed using cutadapt 1.18 and aligned with STAR 2.6.1 (Dobin et al., 2013).
Putative reference cenRNA transcripts were defined from replicate 1 and 2 alignments by reference-guided transcript assembly using Cufflinks (Trapnell et al., 2012). Cufflinks was then used to estimate their abundances in units of FPKM across all samples.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file of centromeric transcript abundaces in each sample, in units of fragments per kilobase per million mapped reads (FPKM).

source_name: HeLa cells

growth_protocol: HeLa and SW480 cells were grown at 37°C, 5% CO2, in Dulbecco's modified Eagle's medium high in glucose and L-glutamine (#11965; Thermo Fisher Scientific/Gibco, Grand Island, NY) supplemented with 10% Fetal Bovine Serum (#26140-079; Thermo Fisher Scientific/Gibco) and 1X Pen/Strep solution (#10378-016; Thermo Fisher Scientific/Gibco).

extract_protocol:
Illumina (IP-202-1012 & IP-202-1024)
RNAs associated to CENP-A or agarose bead (mock-IP) were purified and identified following the protocol described in (Quenet, et al., (2016) Methods Enzymol, 573, 445-466). Briefly, for each condition, five F175 flasks of HeLa cells at a final confluency of 80% were used per RIP-seq. Trypsinized cells were washed two times with cold 1X PBS; 0.1% Tween 20 (#P2287, Sigma-Aldrich), before fixation with 0.1% formaldehyde (#15680, Electron Microscopy Sciences, Hatfield, PA) in 1X PBS. The reaction was stopped by addition of 125mM glycine (#50046, Sigma-Aldrich). Then, nuclei were isolated in TM2 buffer (20mM Tris–HCl, pH 8.0 (#15568-025, Thermo Fisher Scientific); 2mM MgCl2 (#AM9530G, Thermo Fisher Scientific); 0.5mM PMSF (#78830, Sigma-Aldrich); 1X complete protease inhibitor cocktail (#05892953001, Roche, Indianapolis, IN) complemented with 0.5% NonidetTM P40 Substitute (NP40, #74385, Sigma-Aldrich) and 10mM Ribonucleoside Vanadyl Complex (RVC, #1402, New England Biolabs—NEB, Ipswich, MA), and washed in TM2 buffer complemented with 10mM RVC. Chromatin was MNase-digested (MNase, #N3755, Sigma-Aldrich) in 0.1M TE buffer (0.1M NaCl (#24740-011, Thermo Fisher Scientific); 10mM Tris–HCl, pH 8.0; 0.2mM EGTA (#03777, Sigma-Aldrich) in presence of 2mM CaCl2 (#746495, Sigma-Aldrich). After addition of 10mM EGTA to stop the MNase action, nuclear pellet was resuspended in 1mL low-salt buffer (0.5X PBS, 5mM EGTA, 0.5mM PMSF, 1X complete protease inhibitor cocktail) complemented with 50 units of murine RNase inhibitor (#M0314S, NEB), and chromatin was extracted overnight at 4°C in an end-over-end rotator. After centrifugation, the supernatant was precleared with 30μL of protein A/G Plus agarose beads (#sc-2003,Santa Cruz Biotechnology, Dallas, TX) for 30 min at 4°C in an end-over-end rotator, and then, incubated with the anti-CENP-A primary antibody or no antibody for a minimum of 4 hours and a maximum of 12 hours at 4°C in an end-over-end rotator. CENP-A/primary antibody complex and mock-IP sample were immunoprecipitated with 50μL of protein A/G plus agarose beads for 2 hours at 4°C on the end-over-end rotator. Beads were washed three times with 1mL low-salt buffer containing murine RNase inhibitor and complete protease inhibitor cocktail. To isolate immuno-precipitated RNA, RNA–protein complex was eluted (elution buffer: 1% SDS; 0.1M sodium bicarbonate (#S6014, Sigma-Aldrich), denaturated, treated sequentially with proteinase K (#AM2548, Thermo Fisher Scientific/Ambion) and DNaseI (#AM2222, Thermo Fisher Scientific/Ambion), and purified by phenol:chloroform:isoamylalcohol method. RNA concentration was determined by measurement on a UV-spectrophotometer and the quality of RNA was verified using a Bioanalyzer (#5067-1511, Agilent Technologies, Santa Clara, CA).
To prepare RIP samples for sequencing, libraries were constructed using Illumina TruSeq ChIP Library Preparation Kit (IP-202-1012 & IP-202-1024, Illumina, San Diego, CA). RIP libraries were barcoded and run in multiplex on a HiSeq 2500 instrument (Illumina) by the NCI-Sequencing Core Facility. Cluster generation was performed using an Illumina HiSeq PE Cluster Kit v4 cBot (#PE-401-4001, Illumina). The sequencer was run for 125 cycles in paired-end mode. Libraries for SW480 samples and replicates 3 and 4 of HeLa were constructed with the Illumina TruSeq Stranded Total RNA Library Prep protocol, including rRNA depletion. These libraries were sequenced on an Illumina HiSeq4000 instrument for 150 cycles in paired-end mode.

treatment_protocol: Cells were synchronized by double thymidine block (0.5mM, #T9250; Sigma-Aldrich, Saint Louis, MO). After a first block of 19 hours, cells were released for 9 hours, followed by a second thymidine block of 16 hours. Then, cells were released for the appropriate time (10 hours for mitosis and 11 hours for early G1, as described previously in Quenet and Dalal, 2014).

tag: differentiation stage

value: early G1

tag: antibody

value: anti-CENP-A “3-19” [ab13939] (Abcam)

tag: fraction

value: chromatin

tag: treatment

value: alpha-satellite shRNA


title: Input_sh


title: R3_D09_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D09_amb_M82_root_Pool1_LnRep1.fq.gz

tag: cultivar


title: R3_D06_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_M82_shoot_Pool2_LnRep4.fq.gz

tag: day


title: IP_CENPA_sha


title: R3_D06_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_M82_shoot_Pool2_LnRep3.fq.gz

tag: r


title: D06_penn_TRAP_ele-21 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-21_S28_L005_R1_001

tag: pool


title: Input_rep2


title: D12_penn_TRAP_amb-20 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-20_S27_L005_R1_001

tag: lnrep


title: R3_D06_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_M82_shoot_Pool1_LnRep1.fq.gz

tag: tissue


title: D12_penn_TRAP_amb-19 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-19_S26_L005_R1_001


title: R3_D06_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_M82_root_Pool2_LnRep4.fq.gz


title: R3_D06_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_M82_root_Pool2_LnRep3.fq.gz


title: R3_D06_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_M82_root_Pool2_LnRep1.fq.gz


title: IP_CENPA_rep2


title: D12_penn_TRAP_ele-16 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-16_S23_L005_R1_001


title: R3_D06_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_M82_root_Pool1_LnRep1.fq.gz


title: R3_D06_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_M82_root_Pool2_LnRep2.fq.gz


title: R3_D06_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: IP_mock_nucleoplasm_rep1


title: IP_mock_rep1

value: nucleoplasm


title: D12_penn_TRAP_amb-10 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-10_S17_L005_R1_001


title: D06_penn_TRAP_ele-15 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-15_S22_L005_R1_001


title: R3_D06_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R3_D06_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R3_D06_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R3_D06_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: R3_D06_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_M82_root_Pool2_LnRep4.fq.gz


title: IP_CENPA_rep1


title: R3_D06_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_M82_root_Pool2_LnRep3.fq.gz


title: R3_D06_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: D06_penn_TRAP_amb-06 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-06_S13_L005_R1_001


title: IP_mock_rep2


title: R3_D06_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_M82_root_Pool2_LnRep2.fq.gz


title: R3_D06_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_M82_root_Pool2_LnRep1.fq.gz


title: R3_D06_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: A921C10_WGS rep1

source_name: WGS

tag: tissue soure

value: Retina, eye; pigmented epithelium


title: D06_penn_TRAP_amb-02 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-02_S9_L005_R1_001


title: R3_D06_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R3_D06_amb_M82_root_Pool1_LnRep1.fq.gz


title: D12_penn_TRAP_amb-09 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-09_S16_L005_R1_001


title: R5_D12_ele_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_penn_shoot_Pool2_LnRep4.fq.gz


title: R2_D12_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_M82_shoot_Pool2_LnRep3.fq.gz


title: D06_penn_TRAP_ele-05 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-05_S12_L005_R1_001


title: A921C07_CENP-C Cut&Run-seq rep1

source_name: CENP-C Cut&Run-seq


title: R2_D12_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R2_D12_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_M82_shoot_Pool2_LnRep4.fq.gz


title: R2_D12_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R2_D12_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_M82_root_Pool2_LnRep4.fq.gz


title: R2_D12_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: A921C03_CENP-A Cut&Run-seq

source_name: CENP-A Cut&Run-seq


title: R2_D12_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_M82_root_Pool2_LnRep2.fq.gz


title: D06_penn_TRAP_ele-01 (TRAP-Seq)

description:
TRAP_RawGeneCounts.csv
SG-TRAP-01_S8_L005_R1_001


title: R2_D12_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_M82_root_Pool2_LnRep3.fq.gz


title: A1102C18_WGS rep4


title: R5_D12_ele_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_penn_shoot_Pool2_LnRep2.fq.gz


title: A921C11_WGS rep2


title: R2_D12_ele_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_M82_root_Pool1_LnRep1.fq.gz


title: A1102C17_CENP-C Cut&Run-seq rep3


title: IP_CENPA_nucleoplasm_rep1


title: R5_D12_ele_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_penn_shoot_Pool2_LnRep1.fq.gz


title: A921C05_CENP-B Cut&Run-seq rep1

source_name: CENP-B Cut&Run-seq


title: R2_D12_amb_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_M82_shoot_Pool2_LnRep4.fq.gz


title: A1102C16_CENP-C Cut&Run-seq rep2


title: R2_D12_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_M82_shoot_Pool2_LnRep3.fq.gz


title: R5_D12_ele_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_penn_shoot_Pool1_LnRep1.fq.gz


title: R2_D12_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R2_D12_amb_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_M82_shoot_Pool2_LnRep1.fq.gz


title: R5_D12_ele_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_penn_shoot_Pool2_LnRep3.fq.gz


title: A1102C14_WGS rep3


title: R2_D12_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_ele_M82_root_Pool2_LnRep1.fq.gz


title: R5_D12_ele_penn_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_penn_root_Pool2_LnRep4.fq.gz


title: A1102C15_CENP-B Cut&Run-seq rep3


title: R5_D12_ele_penn_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_penn_root_Pool2_LnRep3.fq.gz


title: R2_D12_amb_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_M82_shoot_Pool1_LnRep1.fq.gz


title: A1102C13_CENP-B Cut&Run-seq rep2


title: R5_D12_ele_penn_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_penn_root_Pool2_LnRep2.fq.gz


title: R5_D12_ele_penn_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_penn_root_Pool2_LnRep1.fq.gz


title: R2_D12_amb_M82_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_M82_root_Pool1_LnRep1.fq.gz


title: R2_D12_amb_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_M82_root_Pool2_LnRep1.fq.gz


title: R2_D12_amb_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_M82_root_Pool2_LnRep2.fq.gz


title: R2_D09_ele_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_M82_shoot_Pool2_LnRep3.fq.gz


title: R2_D09_ele_M82_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_M82_shoot_Pool2_LnRep4.fq.gz


title: R2_D09_ele_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_M82_shoot_Pool2_LnRep2.fq.gz


title: R5_D12_ele_penn_root_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_ele_penn_root_Pool1_LnRep1.fq.gz


title: R2_D09_ele_M82_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_M82_shoot_Pool2_LnRep1.fq.gz


title: R2_D09_ele_M82_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_M82_shoot_Pool1_LnRep1.fq.gz


title: R2_D09_ele_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_M82_root_Pool2_LnRep3.fq.gz


title: R2_D09_ele_M82_root_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_M82_root_Pool2_LnRep2.fq.gz


title: R5_D12_amb_penn_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_penn_shoot_Pool2_LnRep3.fq.gz


title: R5_D12_amb_penn_shoot_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_penn_shoot_Pool2_LnRep4.fq.gz


title: R2_D09_ele_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_M82_root_Pool2_LnRep4.fq.gz


title: R2_D12_amb_M82_root_Pool2_LnRep4 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_M82_root_Pool2_LnRep4.fq.gz


title: R5_D12_amb_penn_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_penn_shoot_Pool2_LnRep2.fq.gz


title: R2_D12_amb_M82_root_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D12_amb_M82_root_Pool2_LnRep3.fq.gz


title: R2_D09_ele_M82_root_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_ele_M82_root_Pool2_LnRep1.fq.gz


title: R5_D12_amb_penn_shoot_Pool2_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_penn_shoot_Pool2_LnRep1.fq.gz


title: R5_D12_amb_penn_shoot_Pool1_LnRep1 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R5_D12_amb_penn_shoot_Pool1_LnRep1.fq.gz


title: R2_D09_amb_M82_shoot_Pool2_LnRep2 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_M82_shoot_Pool2_LnRep2.fq.gz


title: R2_D09_amb_M82_shoot_Pool2_LnRep3 (RNA-Seq)

description:
total_unaggregated-480techreps_RawGeneCounts.csv
R2_D09_amb_M82_shoot_Pool2_LnRep3.fq.gz